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SCENIC:cisTarget databases数据库下载

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List of databases for the cisTarget family of tools (e.g. RcisTarget, SCENIC/pySCENIC, and cisTopic).

To choose the database appropiate for your analysis, start by selecting the species and ranking type (i.e. What do you want to analyze: genes or regions?).

Note that the download size is typically over 1GB (100GB for mammal region databases), we recommend downloading the files with zsync_curl (see the Help with downloads).

Related files:

  • sha256sum.txt: To confirm whether the file was succesfuly downloaded
  • TF annotation: Annotation to transcripton factors for the motifs or ChIP-seq tracks in each collection (30-100 Mb)
    • Human TFs (motif collection v8 / v9); (ChIP-seq v1 hg19 / hg38)
    • Mouse TFs (motif collection v8 / v9)
    • Fly TFs (motif collection v8 / v9); (ChIP-seq v1 dm6)

Column info:

Species:

  • Human (Homo sapiens)
  • Mouse (Mus musculus)
  • Fly (Drosophila melanogaster)

Ranking type:

  • Region: The ranking contains regions (i.e. for analyses of region-sets from ATAC-seq, ChIP-seq, …)
  • Genes: The ranking contains genes.

Distance: For gene rankings only. Indicates the search space around the TSS of gene in which the motif is scored:

  • 500bpUp: 500bp upstream of TSS
  • TSS+/-10kb: 10kb around the TSS (total: 20kb)
  • TSS+/-5kb: 5kb around the TSS (total: 10kb)
  • 5kbUp,FullTx: 5kb upstream TSS and transcript introns
  • 500bpUp100Dw: 500bp upstream of TSS, and 100bp downstream.

Motif or track collection:

  • Motifs – Version 8 (mc8nr): 20003 motifs
  • Motifs – Version 9 (mc9nr): 24453 motifs
  • TF ChIP-seq – Version 1 (tc_v1):
    • dm6: 1503 tracks
    • hg19: 3040 tracks
    • hg38: 2993 tracks

nOrt: Number of orthologous species used to select the regions based on conservation. In case of doubt of which version to use: 7 species is normally appropiate for most analyses.

Genome: Genome version used to construct the ranking. For region-based analyses it is important that this version matches your data! Gene annotation version is shown in parenthesis.

Database name: Database name (add the extensions to obtain specific file names, e.g. .feather or .feather.zsync).

Download URL: Link to the database (.feather file, and its size).

List of databases:

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